Doses of Gsk3 Inhibitor :0,1.5,3,6,12,24 uM
Treatment durtaion : 30 min
Quantification steps :
I use the mean signal of each gel to normalize the signal values across the gels : I had done it by two methods to cross-chek results.Both give almost the same values. I have selected M2 for plotting :
M1 : I divide Signal by total(protein/stain) for each well. Then I normalize each of these Signal_by_Total over the mean Signal_by_Total.
M2 : I divide Signal of each well by mean signal for the gel. Similarly,I divide total(protein/stain) of each well by mean total(protein/stain) for the gel. Then I divide normalized signal for each well over the normalized total(protein/stain) for that well.
## Loading required package: lattice
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## mutate
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## intersect, setdiff, setequal, union
## Warning in dir.create("./OutputFiles"): './OutputFiles' already exists
Function ReadInWBData : In case of GSK3i_pAkt, need leave out some lanes since there was a smear in Gel23.
I am using only the mean of R3 samples on Gel23 & only the mean of R2 samples on Gel22. In other cases I’ll use the mean of the whole gel as long as the samples on each of the gels from which data is aggregated are the same.
Gel1(R1)
image_files = c("0001720_02_JuneGel1_CTDR_Aktp.png")
knitr::include_graphics(file.path(image_folder,image_files[1]))
Gel22(R2)
image_files = c("0000062_02_JuneGel22_CTDR_Aktp.png")
knitr::include_graphics(file.path(image_folder,image_files[1]))
Gel23(R3)
image_files = c("0000063_02_JuneGel23_CTDR_Aktp.png")
knitr::include_graphics(file.path(image_folder,image_files[1]))
pAkt_Akt : Reading in Data, Normalization and FC calculation pAkt_Akt : Reading in Data, Normalization and FC calculation
Raw values : Phospho protein and total protein
In Gel23 , there are values for only 17 wells, because two lanes that had smears were not inluded. However the lane number is not corretly specified since, this plot was just an exploratory plot made for myself.
########## Normalization over Common sample
# Plot_RawValues(CTDR_Akt_NormOCom_all,
# Well_no,
# phosP,
# Mean_Com_phosP)
#
# Plot_RawValues(CTDR_Akt_NormOCom_all,
# Well_no,
# totalP,
# Mean_Com_totalP)
Normalization : Over Common Sample and over mean of replicate
########## Normalization over Common sample
#
# Plot_NormValues_Check(CTDR_Akt_NormOCom_all,
# Well_no,
# phosP_Norm_oCom)
########## Normalization over Mean
# Plot_NormValues_Check(CTDR_Akt_NormOMeanRep,
# Well_no,
# phosP_Norm_oMeanRep)
M1 and M2
Plot_NormValues_Check(CTDR_Akt_NormOMeanRep,
Well_no,
Norm_phosP_by_total_M1)
Plot_NormValues_Check(CTDR_Akt_NormOMeanRep,
Well_no,
Norm_phosP_by_total_M2)
T-test:Unpaired
Ttest_pAkt_CTDR_Unpaired <- compare_means(Norm_phosP_by_total_M2 ~ Cell_line,
data = CTDR_Akt_plot,
method = "t.test",
paired = FALSE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pAkt_CTDR_Unpaired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | Norm_phosP_by_total_M2 | XX | XO | 0.0068780 | 0.041 | 0.0069 | ** | T-test |
| 1.5 | Norm_phosP_by_total_M2 | XX | XO | 0.0698290 | 0.130 | 0.0698 | ns | T-test |
| 3.0 | Norm_phosP_by_total_M2 | XX | XO | 0.0190169 | 0.057 | 0.0190 | * | T-test |
| 6.0 | Norm_phosP_by_total_M2 | XX | XO | 0.0088535 | 0.041 | 0.0089 | ** | T-test |
| 12.0 | Norm_phosP_by_total_M2 | XX | XO | 0.0072185 | 0.041 | 0.0072 | ** | T-test |
| 24.0 | Norm_phosP_by_total_M2 | XX | XO | 0.0654411 | 0.130 | 0.0654 | ns | T-test |
Treatment Dose in Log2 scale log2(Treatment+1)
Treatment Doses as Factors
T-test:Unpaired
# Ttest_pAkt_CTDR_Unpaired <- compare_means(Norm_phosP_by_total_M1 ~ Cell_line,
# data = CTDR_Akt_plot,
# method = "t.test",
# paired = FALSE,
# group.by = c("Treatment"),
# ref.group = NULL)
#
# kable(Ttest_pAkt_CTDR_Unpaired)
T-test:Paired
# Ttest_pAkt_CTDR_Paired <- compare_means(Norm_phosP_by_total_M1 ~ Cell_line,
# data = CTDR_Akt_plot,
# method = "t.test",
# paired = TRUE,
# group.by = c("Treatment"),
# ref.group = NULL)
#
# kable(Ttest_pAkt_CTDR_Paired)
Treatment Dose in Log2 scale log2(Treatment+1)
Treatment Doses as Factors
T-test:Unpaired
Ttest_pAkt_CTDR_Unpaired <- compare_means(FCoXX_M2 ~ Cell_line,
data = CTDR_Akt_plot,
method = "t.test",
paired = FALSE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pAkt_CTDR_Unpaired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | FCoXX_M2 | XX | XO | 0.0068780 | 0.041 | 0.0069 | ** | T-test |
| 1.5 | FCoXX_M2 | XX | XO | 0.0698290 | 0.130 | 0.0698 | ns | T-test |
| 3.0 | FCoXX_M2 | XX | XO | 0.0190169 | 0.057 | 0.0190 | * | T-test |
| 6.0 | FCoXX_M2 | XX | XO | 0.0088535 | 0.041 | 0.0089 | ** | T-test |
| 12.0 | FCoXX_M2 | XX | XO | 0.0072185 | 0.041 | 0.0072 | ** | T-test |
| 24.0 | FCoXX_M2 | XX | XO | 0.0654411 | 0.130 | 0.0654 | ns | T-test |
Treatment Dose in Log2 scale log2(Treatment+1)
Treatment Doses as Factors
T-test:Unpaired
Ttest_pAkt_CTDR_Unpaired <- compare_means(FCoXX_M1 ~ Cell_line,
data = CTDR_Akt_plot,
method = "t.test",
paired = FALSE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pAkt_CTDR_Unpaired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | FCoXX_M1 | XX | XO | 0.0045633 | 0.023 | 0.0046 | ** | T-test |
| 1.5 | FCoXX_M1 | XX | XO | 0.0749742 | 0.150 | 0.0750 | ns | T-test |
| 3.0 | FCoXX_M1 | XX | XO | 0.0172491 | 0.069 | 0.0172 | * | T-test |
| 6.0 | FCoXX_M1 | XX | XO | 0.0022758 | 0.014 | 0.0023 | ** | T-test |
| 12.0 | FCoXX_M1 | XX | XO | 0.0267937 | 0.080 | 0.0268 | * | T-test |
| 24.0 | FCoXX_M1 | XX | XO | 0.0869214 | 0.150 | 0.0869 | ns | T-test |
T-test:Paired
Ttest_pAkt_CTDR_Paired <- compare_means(FCoXX_M1 ~ Cell_line,
data = CTDR_Akt_plot,
method = "t.test",
paired = TRUE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pAkt_CTDR_Paired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | FCoXX_M1 | XX | XO | 0.0102556 | 0.062 | 0.010 | * | T-test |
| 1.5 | FCoXX_M1 | XX | XO | 0.1807821 | 0.210 | 0.181 | ns | T-test |
| 3.0 | FCoXX_M1 | XX | XO | 0.1042327 | 0.210 | 0.104 | ns | T-test |
| 6.0 | FCoXX_M1 | XX | XO | 0.0322956 | 0.160 | 0.032 | * | T-test |
| 12.0 | FCoXX_M1 | XX | XO | 0.0444666 | 0.180 | 0.044 | * | T-test |
| 24.0 | FCoXX_M1 | XX | XO | 0.0472210 | 0.180 | 0.047 | * | T-test |
Treatment Dose in Log2 scale log2(Treatment+1)
Treatment Doses as Factors
T-test:Unpaired This comparison gave an error because the control replicate values were 1 ??
Ttest_pAkt_CTDR_Unpaired <- compare_means(FCoCntrl_M2 ~ Cell_line,
data = CTDR_Akt_plot,
method = "t.test",
paired = FALSE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pAkt_CTDR_Unpaired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | FCoCntrl_M2 | XX | XO | 1.0000000 | 1 | 1.00 | ns | T-test |
| 1.5 | FCoCntrl_M2 | XX | XO | 0.6895333 | 1 | 0.69 | ns | T-test |
| 3.0 | FCoCntrl_M2 | XX | XO | 0.6187675 | 1 | 0.62 | ns | T-test |
| 6.0 | FCoCntrl_M2 | XX | XO | 0.8166795 | 1 | 0.82 | ns | T-test |
| 12.0 | FCoCntrl_M2 | XX | XO | 0.4948997 | 1 | 0.49 | ns | T-test |
| 24.0 | FCoCntrl_M2 | XX | XO | 0.9457132 | 1 | 0.95 | ns | T-test |
Treatment Dose in Log2 scale log2(Treatment+1)
Treatment Doses as Factors
T-test:Unpaired This comparison gave an error because the control replicate values were 1 ??
Ttest_pAkt_CTDR_Unpaired <- compare_means(FCoCntrl_M1 ~ Cell_line,
data = CTDR_Akt_plot,
method = "t.test",
paired = FALSE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pAkt_CTDR_Unpaired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | FCoCntrl_M1 | XX | XO | 1.0000000 | 1 | 1.00 | ns | T-test |
| 1.5 | FCoCntrl_M1 | XX | XO | 0.6792163 | 1 | 0.68 | ns | T-test |
| 3.0 | FCoCntrl_M1 | XX | XO | 0.5896125 | 1 | 0.59 | ns | T-test |
| 6.0 | FCoCntrl_M1 | XX | XO | 0.7732120 | 1 | 0.77 | ns | T-test |
| 12.0 | FCoCntrl_M1 | XX | XO | 0.5573437 | 1 | 0.56 | ns | T-test |
| 24.0 | FCoCntrl_M1 | XX | XO | 0.9480569 | 1 | 0.95 | ns | T-test |
T-test:Paired
Ttest_pAkt_CTDR_Paired <- compare_means(FCoCntrl_M1 ~ Cell_line,
data = CTDR_Akt_plot,
method = "t.test",
paired = TRUE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pAkt_CTDR_Paired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | FCoCntrl_M1 | XX | XO | 1.0000000 | 1 | 1.00 | ns | T-test |
| 1.5 | FCoCntrl_M1 | XX | XO | 0.7644804 | 1 | 0.76 | ns | T-test |
| 3.0 | FCoCntrl_M1 | XX | XO | 0.7095662 | 1 | 0.71 | ns | T-test |
| 6.0 | FCoCntrl_M1 | XX | XO | 0.8247507 | 1 | 0.82 | ns | T-test |
| 12.0 | FCoCntrl_M1 | XX | XO | 0.5961830 | 1 | 0.60 | ns | T-test |
| 24.0 | FCoCntrl_M1 | XX | XO | 0.8566883 | 1 | 0.86 | ns | T-test |
Treatment Dose in Log2 scale log2(Treatment+1)
Treatment Doses as Factors
Gel3(R1), Gel19(R2) and Gel20(R3)
image_files = c("0001725_02_JuneGel3_CTDR_p70S6K.png","0000584_02_JuneGel3_CTDR_TPS.png")
knitr::include_graphics(file.path(image_folder,image_files[1]))
knitr::include_graphics(file.path(image_folder,image_files[2]))
image_files = c("0000044_02_JuneGel19_CTDR_p70S6K.png","0000048_02_JuneGel19_CTDR_TPS.png")
knitr::include_graphics(file.path(image_folder,image_files[1]))
knitr::include_graphics(file.path(image_folder,image_files[2]))
image_files = c("0000045_02_JuneGel20_CTDR_p70S6K.png","0000049_02_JuneGel20_CTDR_TPS.png")
knitr::include_graphics(file.path(image_folder,image_files[1]))
knitr::include_graphics(file.path(image_folder,image_files[2]))
pP70s6k_TPS : Reading in Data, Normalization and FC calculation
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## * ...
Raw values : Phospho protein and total protein
########## Normalization over Common sample
# Plot_RawValues(CTDR_P70s6k_NormOCom_all,
# Well_no,
# phosP,
# Mean_Com_phosP)
#
# Plot_RawValues(CTDR_P70s6k_NormOCom_all,
# Well_no,
# totalP,
# Mean_Com_totalP)
Normalization : Over Common Sample and over mean of replicate
For “Over Common Sample” : There were two samples that were on both gels(19 and 20). These were the untreated controls of both XX and XO cell line of Replicate1. So the mean of these common samples was used for normalization.
########## Normalization over Common sample
# Plot_NormValues_Check(CTDR_P70s6k_NormOCom_all,
# Well_no,
# phosP_Norm_oCom)
#
#
# ########## Normalization over Mean
#
# Plot_NormValues_Check(CTDR_P70s6k_NormOMeanRep,
# Well_no,
# phosP_Norm_oMeanRep)
M1 and M2
Plot_NormValues_Check(CTDR_P70s6k_NormOMeanRep,
Well_no,
Norm_phosP_by_total_M1)
Plot_NormValues_Check(CTDR_P70s6k_NormOMeanRep,
Well_no,
Norm_phosP_by_total_M2)
T-test:Unpaired
Ttest_pP70s6k_CTDR_Unpaired <- compare_means(Norm_phosP_by_total_M2 ~ Cell_line,
data = CTDR_P70s6k_plot,
method = "t.test",
paired = FALSE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pP70s6k_CTDR_Unpaired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | Norm_phosP_by_total_M2 | XX | XO | 0.4676918 | 1 | 0.47 | ns | T-test |
| 1.5 | Norm_phosP_by_total_M2 | XX | XO | 0.4010295 | 1 | 0.40 | ns | T-test |
| 3.0 | Norm_phosP_by_total_M2 | XX | XO | 0.3207886 | 1 | 0.32 | ns | T-test |
| 6.0 | Norm_phosP_by_total_M2 | XX | XO | 0.9346933 | 1 | 0.93 | ns | T-test |
| 12.0 | Norm_phosP_by_total_M2 | XX | XO | 0.4274391 | 1 | 0.43 | ns | T-test |
| 24.0 | Norm_phosP_by_total_M2 | XX | XO | 0.3300841 | 1 | 0.33 | ns | T-test |
Treatment Dose in Log2 scale log2(Treatment+1)
Treatment Doses as Factors
T-test:Unpaired
Ttest_pP70s6k_CTDR_Unpaired <- compare_means(Norm_phosP_by_total_M1 ~ Cell_line,
data = CTDR_P70s6k_plot,
method = "t.test",
paired = FALSE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pP70s6k_CTDR_Unpaired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | Norm_phosP_by_total_M1 | XX | XO | 0.4698484 | 1 | 0.47 | ns | T-test |
| 1.5 | Norm_phosP_by_total_M1 | XX | XO | 0.3783957 | 1 | 0.38 | ns | T-test |
| 3.0 | Norm_phosP_by_total_M1 | XX | XO | 0.3201212 | 1 | 0.32 | ns | T-test |
| 6.0 | Norm_phosP_by_total_M1 | XX | XO | 0.9376913 | 1 | 0.94 | ns | T-test |
| 12.0 | Norm_phosP_by_total_M1 | XX | XO | 0.4373032 | 1 | 0.44 | ns | T-test |
| 24.0 | Norm_phosP_by_total_M1 | XX | XO | 0.3378120 | 1 | 0.34 | ns | T-test |
T-test:Paired
Ttest_pP70s6k_CTDR_Paired <- compare_means(Norm_phosP_by_total_M1 ~ Cell_line,
data = CTDR_P70s6k_plot,
method = "t.test",
paired = TRUE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pP70s6k_CTDR_Paired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | Norm_phosP_by_total_M1 | XX | XO | 0.4811580 | 1 | 0.48 | ns | T-test |
| 1.5 | Norm_phosP_by_total_M1 | XX | XO | 0.5266256 | 1 | 0.53 | ns | T-test |
| 3.0 | Norm_phosP_by_total_M1 | XX | XO | 0.3120085 | 1 | 0.31 | ns | T-test |
| 6.0 | Norm_phosP_by_total_M1 | XX | XO | 0.9568264 | 1 | 0.96 | ns | T-test |
| 12.0 | Norm_phosP_by_total_M1 | XX | XO | 0.4704039 | 1 | 0.47 | ns | T-test |
| 24.0 | Norm_phosP_by_total_M1 | XX | XO | 0.4570191 | 1 | 0.46 | ns | T-test |
Treatment Dose in Log2 scale log2(Treatment+1)
Treatment Doses as Factors
T-test:Unpaired
Ttest_pP70s6k_CTDR_Unpaired <- compare_means(FCoXX_M2 ~ Cell_line,
data = CTDR_P70s6k_plot,
method = "t.test",
paired = FALSE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pP70s6k_CTDR_Unpaired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | FCoXX_M2 | XX | XO | 0.4676918 | 1 | 0.47 | ns | T-test |
| 1.5 | FCoXX_M2 | XX | XO | 0.4010295 | 1 | 0.40 | ns | T-test |
| 3.0 | FCoXX_M2 | XX | XO | 0.3207886 | 1 | 0.32 | ns | T-test |
| 6.0 | FCoXX_M2 | XX | XO | 0.9346933 | 1 | 0.93 | ns | T-test |
| 12.0 | FCoXX_M2 | XX | XO | 0.4274391 | 1 | 0.43 | ns | T-test |
| 24.0 | FCoXX_M2 | XX | XO | 0.3300841 | 1 | 0.33 | ns | T-test |
Treatment Dose in Log2 scale log2(Treatment+1)
Treatment Doses as Factors
T-test:Unpaired
Ttest_pP70s6k_CTDR_Unpaired <- compare_means(FCoXX_M1 ~ Cell_line,
data = CTDR_P70s6k_plot,
method = "t.test",
paired = FALSE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pP70s6k_CTDR_Unpaired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | FCoXX_M1 | XX | XO | 0.4698484 | 1 | 0.47 | ns | T-test |
| 1.5 | FCoXX_M1 | XX | XO | 0.3783957 | 1 | 0.38 | ns | T-test |
| 3.0 | FCoXX_M1 | XX | XO | 0.3201212 | 1 | 0.32 | ns | T-test |
| 6.0 | FCoXX_M1 | XX | XO | 0.9376913 | 1 | 0.94 | ns | T-test |
| 12.0 | FCoXX_M1 | XX | XO | 0.4373032 | 1 | 0.44 | ns | T-test |
| 24.0 | FCoXX_M1 | XX | XO | 0.3378120 | 1 | 0.34 | ns | T-test |
T-test:Paired
Ttest_pP70s6k_CTDR_Paired <- compare_means(FCoXX_M1 ~ Cell_line,
data = CTDR_P70s6k_plot,
method = "t.test",
paired = TRUE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pP70s6k_CTDR_Paired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | FCoXX_M1 | XX | XO | 0.4811580 | 1 | 0.48 | ns | T-test |
| 1.5 | FCoXX_M1 | XX | XO | 0.5266256 | 1 | 0.53 | ns | T-test |
| 3.0 | FCoXX_M1 | XX | XO | 0.3120085 | 1 | 0.31 | ns | T-test |
| 6.0 | FCoXX_M1 | XX | XO | 0.9568264 | 1 | 0.96 | ns | T-test |
| 12.0 | FCoXX_M1 | XX | XO | 0.4704039 | 1 | 0.47 | ns | T-test |
| 24.0 | FCoXX_M1 | XX | XO | 0.4570191 | 1 | 0.46 | ns | T-test |
Treatment Dose in Log2 scale log2(Treatment+1)
Treatment Doses as Factors
T-test:Unpaired This comparison gave an error because the control replicate values were 1 ??
Ttest_pP70s6k_CTDR_Unpaired <- compare_means(FCoCntrl_M2 ~ Cell_line,
data = CTDR_P70s6k_plot,
method = "t.test",
paired = FALSE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pP70s6k_CTDR_Unpaired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | FCoCntrl_M2 | XX | XO | 1.0000000 | 1.00 | 1.00 | ns | T-test |
| 1.5 | FCoCntrl_M2 | XX | XO | 0.1872044 | 0.83 | 0.19 | ns | T-test |
| 3.0 | FCoCntrl_M2 | XX | XO | 0.2393350 | 0.83 | 0.24 | ns | T-test |
| 6.0 | FCoCntrl_M2 | XX | XO | 0.0597904 | 0.36 | 0.06 | ns | T-test |
| 12.0 | FCoCntrl_M2 | XX | XO | 0.2667290 | 0.83 | 0.27 | ns | T-test |
| 24.0 | FCoCntrl_M2 | XX | XO | 0.1662781 | 0.83 | 0.17 | ns | T-test |
Treatment Dose in Log2 scale log2(Treatment+1)
Treatment Doses as Factors
T-test:Unpaired This comparison gave an error because the control replicate values were 1 ??
Ttest_pP70s6k_CTDR_Unpaired <- compare_means(FCoCntrl_M1 ~ Cell_line,
data = CTDR_P70s6k_plot,
method = "t.test",
paired = FALSE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pP70s6k_CTDR_Unpaired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | FCoCntrl_M1 | XX | XO | 1.0000000 | 1.00 | 1.000 | ns | T-test |
| 1.5 | FCoCntrl_M1 | XX | XO | 0.1721236 | 0.85 | 0.172 | ns | T-test |
| 3.0 | FCoCntrl_M1 | XX | XO | 0.2385558 | 0.85 | 0.239 | ns | T-test |
| 6.0 | FCoCntrl_M1 | XX | XO | 0.0324939 | 0.19 | 0.032 | * | T-test |
| 12.0 | FCoCntrl_M1 | XX | XO | 0.2740605 | 0.85 | 0.274 | ns | T-test |
| 24.0 | FCoCntrl_M1 | XX | XO | 0.1708718 | 0.85 | 0.171 | ns | T-test |
T-test:Paired
Ttest_pP70s6k_CTDR_Paired <- compare_means(FCoCntrl_M1 ~ Cell_line,
data = CTDR_P70s6k_plot,
method = "t.test",
paired = TRUE,
group.by = c("Treatment"),
ref.group = NULL)
kable(Ttest_pP70s6k_CTDR_Paired)
| Treatment | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|
| 0.0 | FCoCntrl_M1 | XX | XO | 1.0000000 | 1.00 | 1.00 | ns | T-test |
| 1.5 | FCoCntrl_M1 | XX | XO | 0.3301041 | 1.00 | 0.33 | ns | T-test |
| 3.0 | FCoCntrl_M1 | XX | XO | 0.2324780 | 1.00 | 0.23 | ns | T-test |
| 6.0 | FCoCntrl_M1 | XX | XO | 0.1414416 | 0.85 | 0.14 | ns | T-test |
| 12.0 | FCoCntrl_M1 | XX | XO | 0.3205950 | 1.00 | 0.32 | ns | T-test |
| 24.0 | FCoCntrl_M1 | XX | XO | 0.2911853 | 1.00 | 0.29 | ns | T-test |
Treatment Dose in Log2 scale log2(Treatment+1)
Treatment Doses as Factors
write.csv(CTDR_Akt_FC, file = "OutputFiles/CTDR_Akt_FC.csv")
write.csv(CTDR_P70s6k_FC, file = "OutputFiles/CTDR_P70s6k_FC.csv")
I am using the WB imgaes from R3,
CTDR_All <- dplyr::full_join(CTDR_Akt_plot, CTDR_P70s6k_plot, by=c("Cell_line","Replicate","Treatment","log2Treatment","Treatment_Fctr"), suffix = c("_Akt", "_P70s6k"))
CTDR_All <- CTDR_All %>%
select(-c(grep("Analyte", colnames(CTDR_All))))
CTDR_All$Cell_line <- factor(CTDR_All$Cell_line, levels = c("XX", "XO", "nn"))
CTDR_Allplot <- CTDR_All %>%
select(c("Cell_line","Replicate","Treatment","log2Treatment","Treatment_Fctr",grep("FCoXX_M2",colnames(CTDR_All)))) %>%
gather(key = "Analyte", value = "Signal", -c("Cell_line","Replicate","Treatment","log2Treatment","Treatment_Fctr"))
Analyte_labels <- c("FCoXX_M2_Akt" = "pAkt", "FCoXX_M2_P70s6k" = "pP70s6k")
#### Setting up the plotting attributes ###
# MyCellLineColours <- c("XX" = "#FF0000", "XO" = "#0000CD", "nn" = "#000005")
# MyReplicateShapes <- c("R1" = 2, "R2" = 0, "R3" = 6, "nn"= 4)
g <- Plot_TwoPanel_ValidationPlot_updated(CTDR_Allplot,"log2Treatment", "Signal" ,Analyte_labels,"fixed")+
labs(x = "\nGsk3i(\u03bcM)+1 [log2]", #\u03bc is the unicode charachter fro greek mu
y = "Rel. phosp. (norm.)\n",
color = "Cell line" ) # color within labs,lets me give user defined labels to the attribute in legend
gt=set_panel_size(g,width=unit(2.8,'cm'),height=unit(2.8,'cm'))
grid.arrange(gt)
ggsave("CTDR_pAkt_pP70s6k_FCoXX_s15.pdf", gt, dpi=300, useDingbats=FALSE ,path = "./OutputFiles") # device = cairo_pdf was tried to get the greek letter in pdf, but not yet successful in that
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